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vb_set_head_parm

PURPOSE ^

set head parameters for vb_job_head_3shell

SYNOPSIS ^

function head_parm = vb_set_head_parm

DESCRIPTION ^

 set head parameters for vb_job_head_3shell
    head_parm = vb_set_head_parm;
 --- Setting for Output file  [relative path from 'proj_root']
 head_parm.head_file : Base name for head model
 --- Setting for Output surface
 head_parm.Nsurf   : Number of shell (=1 for MEG , =3 for EEG [default])
 head_parm.Nvertex : number of vertex in each surface 
              = [2000] (Default)

 --- Setting for MRI input file  (Absolute path)
   head_parm.analyze_file : MRI image file

 --- Setting for Scalp input file (Absolute path) [There are 2 cases]
    If the following files are specified at the same time,
    priority order is fs_scalp_file > face_file
 1.  head_parm.face_file     : face file made by vbmeg
 2.  head_parm.fs_scalp_file : FreeSurfer Scalp ('outer_skin_surface.asc')

 --- Setting for CSF input files (Absolute path) [There are 3 cases]
   We recommend to use both FreeSurfer and Segment files:
      'freesurf_file' + 'gray_file' + 'brain_file'

 1. FreeSurfer file Case
   head_parm.freesurf_file : FreeSurfer CSF ('inner_skull_surface.asc')
 2. Segment file Case
   head_parm.brain_file : Brain model file (.brain.mat)
   head_parm.gray_file  : Gray matter segment file made by SPM 'Segment'

 3. Curry file Case
   head_parm.curry_file : Curry surface file

%% --- Advanced Optional Parameter
 parm.Scalp_mode 
     = 0 : Scalp surface is intersection of face and dilated CSF [Default]
     = 1 : Scalp surface is smoothed face & Skull is the same as mode=0
     = 2 : Scalp surface is smoothed face & Skull is erosion of face

 --- Optional setting for outer Skull surface   (Absolute path)
 parm.fs_skull_file : Outer Skull surface ('/outer_skull_surface.asc')

 --- Radius of Morphology operation [mm]
 If the obtained shell model is not good,
 you can adjust the following morphology radius parameters

 parm.Radius_scalp = 4 : Thickness of Scalp [mm]
 parm.Radius_skull = 2 : Min Thickness of Skull [mm]
 parm.Radius_fs  : smoothing radius for FreeSurfer surface
                 = [4 -4 ] Default (No size change)
 parm.Radius_csf : smoothing radius for Gray matter
                 = [6 6 -7 ] Default (Expand 6 mm)
 parm.Radius     : smoothing radius for CSF surface
                 = [4 -4 ] Default (No size change)
 
 parm.Nloop  = 200; Iteration number for fit boundary
 parm.Nlast_csf   = 10 ; Iteration number for CSF smoothing by spring model
                    As Nlast becomes larger, surface becomes smoother
                    but it shrinks inward
 parm.Nlast_scalp  = 0 ; Iteration number for Scalp
 parm.Nlast_skull  = 0 ; Iteration number for Skull
 (Gray matter parameters)
 parm.Glevel      = [0.8];  level of gray matter selection threshold
 parm.Radius_gray = [-2 2]; Radius to remove noise in gray matter image
 (Brain model parameters)
 parm.Radius_fill = [6];    Cortex fill radius

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function    head_parm = vb_set_head_parm
0002 % set head parameters for vb_job_head_3shell
0003 %    head_parm = vb_set_head_parm;
0004 % --- Setting for Output file  [relative path from 'proj_root']
0005 % head_parm.head_file : Base name for head model
0006 % --- Setting for Output surface
0007 % head_parm.Nsurf   : Number of shell (=1 for MEG , =3 for EEG [default])
0008 % head_parm.Nvertex : number of vertex in each surface
0009 %              = [2000] (Default)
0010 %
0011 % --- Setting for MRI input file  (Absolute path)
0012 %   head_parm.analyze_file : MRI image file
0013 %
0014 % --- Setting for Scalp input file (Absolute path) [There are 2 cases]
0015 %    If the following files are specified at the same time,
0016 %    priority order is fs_scalp_file > face_file
0017 % 1.  head_parm.face_file     : face file made by vbmeg
0018 % 2.  head_parm.fs_scalp_file : FreeSurfer Scalp ('outer_skin_surface.asc')
0019 %
0020 % --- Setting for CSF input files (Absolute path) [There are 3 cases]
0021 %   We recommend to use both FreeSurfer and Segment files:
0022 %      'freesurf_file' + 'gray_file' + 'brain_file'
0023 %
0024 % 1. FreeSurfer file Case
0025 %   head_parm.freesurf_file : FreeSurfer CSF ('inner_skull_surface.asc')
0026 % 2. Segment file Case
0027 %   head_parm.brain_file : Brain model file (.brain.mat)
0028 %   head_parm.gray_file  : Gray matter segment file made by SPM 'Segment'
0029 %
0030 % 3. Curry file Case
0031 %   head_parm.curry_file : Curry surface file
0032 %
0033 %%% --- Advanced Optional Parameter
0034 % parm.Scalp_mode
0035 %     = 0 : Scalp surface is intersection of face and dilated CSF [Default]
0036 %     = 1 : Scalp surface is smoothed face & Skull is the same as mode=0
0037 %     = 2 : Scalp surface is smoothed face & Skull is erosion of face
0038 %
0039 % --- Optional setting for outer Skull surface   (Absolute path)
0040 % parm.fs_skull_file : Outer Skull surface ('/outer_skull_surface.asc')
0041 %
0042 % --- Radius of Morphology operation [mm]
0043 % If the obtained shell model is not good,
0044 % you can adjust the following morphology radius parameters
0045 %
0046 % parm.Radius_scalp = 4 : Thickness of Scalp [mm]
0047 % parm.Radius_skull = 2 : Min Thickness of Skull [mm]
0048 % parm.Radius_fs  : smoothing radius for FreeSurfer surface
0049 %                 = [4 -4 ] Default (No size change)
0050 % parm.Radius_csf : smoothing radius for Gray matter
0051 %                 = [6 6 -7 ] Default (Expand 6 mm)
0052 % parm.Radius     : smoothing radius for CSF surface
0053 %                 = [4 -4 ] Default (No size change)
0054 %
0055 % parm.Nloop  = 200; Iteration number for fit boundary
0056 % parm.Nlast_csf   = 10 ; Iteration number for CSF smoothing by spring model
0057 %                    As Nlast becomes larger, surface becomes smoother
0058 %                    but it shrinks inward
0059 % parm.Nlast_scalp  = 0 ; Iteration number for Scalp
0060 % parm.Nlast_skull  = 0 ; Iteration number for Skull
0061 % (Gray matter parameters)
0062 % parm.Glevel      = [0.8];  level of gray matter selection threshold
0063 % parm.Radius_gray = [-2 2]; Radius to remove noise in gray matter image
0064 % (Brain model parameters)
0065 % parm.Radius_fill = [6];    Cortex fill radius
0066 %
0067 % Copyright (C) 2011, ATR All Rights Reserved.
0068 % License : New BSD License(see VBMEG_LICENSE.txt)
0069 
0070 % --- Setting for Output file
0071 % [relative path from 'proj_root']
0072 head_parm.head_file = [];
0073 
0074 % --- Setting for MRI input file
0075 % (Absolute path)
0076 head_parm.analyze_file = 'Subject.nii';
0077 
0078 % --- Setting for Scalp input file [There are 2 cases]
0079 % 1.  head_parm.face_file     : face file made by vbmeg
0080 % 2.  head_parm.fs_scalp_file : FreeSurfer Scalp ('outer_skin_surface.asc')
0081 
0082 % (Absolute path)
0083 % head_parm.face_file = [];
0084 head_parm.fs_scalp_file = 'bem/outer_skin_surface.asc';
0085 
0086 % --- Setting for CSF input files [There are 3 cases]
0087 % 1. FreeSurfer file Case
0088 % 2. Segment file Case
0089 % 3. Curry file Case
0090 %    We recommend to use 'freesurf_file' + 'gray_file' + 'brain_file'
0091 
0092 % Relative path from 'proj_root'
0093 head_parm.brain_file = 'Subject.brain.mat';
0094 
0095 % (Absolute path)
0096 head_parm.freesurf_file = 'bem/inner_skull_surface.asc';
0097 head_parm.gray_file  = 'c1Subject.nii';
0098 %   head_parm.curry_file = [];
0099 
0100 
0101 % Number of surface
0102 % Default is 3 shell model
0103 head_parm.Nsurf = 3;
0104 head_parm.Nvertex = [2000];
0105 
0106 %%% --- Advanced Optional Parameters
0107 %%%     Usually, there is no need to change the following parameters
0108 %%%     In the case where the result is not good, you can try again
0109 %%%     by changing the following parameters
0110 
0111 % Set Default Radius parameters
0112 head_parm.Radius_fs  = [4 -4]; 
0113 head_parm.Radius_csf = [6 6 -7 ] ; 
0114 head_parm.Radius_scalp = 4; 
0115 head_parm.Radius_skull = 2; 
0116 head_parm.Skull_ratio  = 0.5;
0117 
0118 head_parm.Radius     = [4 -4 ] ; 
0119 head_parm.Radius_final = [4 -4];
0120 
0121 head_parm.Radius_fill = [6];     
0122 head_parm.Radius_gray = [-2 2];  
0123 head_parm.Glevel      = [0.8];  
0124 
0125 head_parm.Nloop  = 200;  
0126 
0127 head_parm.Nlast_csf   = 10 ; 
0128 head_parm.Nlast_scalp = 0 ;  
0129 head_parm.Nlast_skull = 0 ;  
0130 
0131 
0132 % Scalp_mode
0133 head_parm.Scalp_mode = 0; 
0134 
0135 % subsampling size for mask image [mm]
0136 if vb_matlab_version > 6,
0137     head_parm.vstep = 1; 
0138 else
0139     head_parm.vstep = 2; 
0140 end
0141

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